[Ecopd-commits] r66 - branches/single-tree

[noreply at r-forge.r-project.org]

Author: regetz
Date: 2009-11-14 02:08:48 +0100 (Sat, 14 Nov 2009)
New Revision: 66

Modified:
   branches/single-tree/DESCRIPTION
   branches/single-tree/NAMESPACE
Log:
updated NAMESPACE; added collate field to DESCRIPTION


Modified: branches/single-tree/DESCRIPTION
===================================================================
--- branches/single-tree/DESCRIPTION	2009-11-14 00:59:20 UTC (rev 65)
+++ branches/single-tree/DESCRIPTION	2009-11-14 01:08:48 UTC (rev 66)
@@ -8,5 +8,6 @@
 Depends: ape, phylobase
 Description: A set of metrics and functions for combining ecological and phylogenetic information
 License: GPL
+Collate: phylo4com.R utilities.R community.R pd.R ed.R iac.R pae.R simpson.R indices.R plots.R
 LazyLoad: yes
 LazyData: yes

Modified: branches/single-tree/NAMESPACE
===================================================================
--- branches/single-tree/NAMESPACE	2009-11-14 00:59:20 UTC (rev 65)
+++ branches/single-tree/NAMESPACE	2009-11-14 01:08:48 UTC (rev 66)
@@ -1,35 +1,48 @@
+#----------------------------------------------------------------------
+
+#importMethodsFrom(phylobase, subset)
+#importMethodsFrom(phylobase, labels)
+import(phylobase)
+
+#----------------------------------------------------------------------
+
+exportClasses(phylo4com)
+
+#----------------------------------------------------------------------
+
+# constructor methods
+exportMethods(phylo4com)
+
+# metric methods
+exportMethods(pd, pae, iac, ed, eed, hed, aed, eaed, haed, value)
+exportMethods(simpson)
+
+#----------------------------------------------------------------------
+
+# phylogeny helper functions
 export(tipLength)
 export(pairdist)
-export(abundance)
-export(`abundance<-`)
-export(minTL)
-export(`minTL<-`)
 
-export(caterpillar)
+# community helper functions
+export(abundance, "abundance<-")
+export(presence)
+export(communities)
 export(genera)
-export(getMinTL)
-export(pd)
 export(richness)
-export(simp.phy)
 export(siteBySpecies)
+
+# pd-related functions
+export(minTL)
+export(`minTL<-`)
+export(getMinTL)
 export(weightByAbund)
 
+# miscellaneous
+export(caterpillar)
+
+# reference data sets
 export(Families)
 export(LookupTL)
 export(Supertree)
 
-export(phylo4com)
-export(pd)
-export(PAE)
-export(IAC)
-export(ED)
-export(EED)
-export(HED)
-export(AED)
-export(EAED)
-export(HAED)
-export(value)
-
-#importMethodsFrom(phylobase, subset)
-#importMethodsFrom(phylobase, labels)
-import(phylobase)
+#----------------------------------------------------------------------